HHsearch alignment for GI: 254780345 and conserved domain: cd00447

>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the
Probab=99.97  E-value=3.7e-29  Score=195.38  Aligned_cols=126  Identities=33%  Similarity=0.425  Sum_probs=117.3

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             99999999999995699989999999985310013221120144343999999999999989999999997410357633
Q gi|254780345|r   19 ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFS   98 (170)
Q Consensus        19 aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~~   98 (170)
T Consensus         2 AR~~a~~~L~~~~~~~~~~~~~l~~~~~-----------~~~l~~~d~~~~~~lv~gv~~~~~~ld~~i~~~l-~~~~~~   69 (129)
T cd00447           2 AREIAFQALYQVEIRNGISLEAVLSALE-----------KLQLAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLD   69 (129)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHH-----------HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHH
T ss_conf             8999999999998209999999999998-----------7789778999999999999996999999999982-788031


Q ss_pred             HCCCHHHHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             235348999999999986435-5781033988999999833877231499999999952
Q gi|254780345|r   99 RLDMILCSILRAGVLELIECH-SVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK  156 (170)
Q Consensus        99 rl~~~~~~iLr~a~~El~~~~-~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~  156 (170)
T Consensus        70 ~~~~i~~~iLrl~~~el~~~~~~ip~~~~InE~v~lak~~~~~~~~~fvNavLr~i~r~  128 (129)
T cd00447          70 RLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE  128 (129)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf             10088899999999999985058985167899999999867886320079997798734